Simple script to calculate what percentage of genes have associated regulatory features.

misc-scripts/regulatory_regions/gene_coverage.pl

+# Check how many genes have regulatory features associated
+
+use strict;
+
+use DBI;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Getopt::Long;
+
+my ($host, $user, $pass, $port, $dbname, $file, $del);
+
+GetOptions( "host=s",   \$host,
+	    "user=s",   \$user,
+	    "pass=s",   \$pass,
+	    "port=i",   \$port,
+	    "dbname=s", \$dbname,
+	    "help",     \&usage);
+
+my $db_adaptor = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
+						    -user => $user,
+						    -port => $port,
+						    -pass => $pass,
+						    -dbname => $dbname);
+
+my $gene_adaptor = $db_adaptor->get_GeneAdaptor();
+
+my @genes = @{$gene_adaptor->list_dbIDs()};
+
+my $total_genes = 0;
+my $genes_with_rf = 0;
+
+$| = 1; # flush after every print
+print "Genes analysed: ";
+
+foreach my $gene_id (@genes) {
+
+  my $gene = $gene_adaptor->fetch_by_dbID($gene_id);
+  $total_genes++;
+  my @features = @{$gene->get_all_regulatory_features(1)};
+  $genes_with_rf++ if (@features);
+  print $total_genes . " " if ($total_genes % 1000 == 0);
+
+}
+
+my $pc = (100 * $genes_with_rf) / $total_genes;
+
+printf "\n\nTotal of %s genes, of which %d (%2.1f%%) have associated regulatory features.\n", $total_genes, $genes_with_rf, $pc;